Antigen

Antigen Class

RNA polymerase

Antigen

RNA polymerase II

Cell type

Cell type Class

Epidermis

Cell type

Melanoma

MeSH Description

A malignant neoplasm derived from cells that are capable of forming melanin, which may occur in the skin of any part of the body, in the eye, or, rarely, in the mucous membranes of the genitalia, anus, oral cavity, or other sites. It occurs mostly in adults and may originate de novo or from a pigmented nevus or malignant lentigo. Melanomas frequently metastasize widely, and the regional lymph nodes, liver, lungs, and brain are likely to be involved. The incidence of malignant skin melanomas is rising rapidly in all parts of the world. (Stedman, 25th ed; from Rook et al., Textbook of Dermatology, 4th ed, p2445)

Sample

source_name

Skin

disease

melanoma

morphology

mixture of spindle-shaped and epithelial-like cells

chip antibody

RNAPII (Active Motif: 39097)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chromatin extrated cell cell lysate was sonicated and shered to 300bp to 1kb fragments using a Sonifier Cell Disruptor (Branson Ultrasonics #101-063-588). To 0.5ml sheared chromatin (after clarification of debrie), we added 150µl ChIP mix (440mM NaCl, 0.44% sodium deoxycholate, 4.4% Triton X-100) and antibody-coupled beads for immunoprecipitation overnight at 4C. Precipitated DNA fragments were processed to ChIP-seq library using the ThruPLEX DNA-seq 12S kit (Takara #R400428) according to manufacturer's instructions. 75bp paired end

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

17144109

Reads aligned (%)

69.0

Duplicates removed (%)

17.7

Number of peaks

15844 (qval < 1E-05)

mm9

Number of total reads

17144109

Reads aligned (%)

68.8

Duplicates removed (%)

18.1

Number of peaks

15785 (qval < 1E-05)